I've never experienced your problems with Sigil. What you can do is use
Mobiunpack to unpack your mobi files and then try to identify the styles that are causing the font size issues.
You could also try to post a small sample .ePub file that has font size issues, when it's converted to .mobi. (Post both the ePub and the mobi files as attachments.)
BTW, did you instal any font hacks on your Kindle?